Archaea, tiny helpers of land plants

Abstract

Archaea are members of most microbiomes. While archaea are highly abundant in extreme environments, they are less abundant and diverse in association with eukaryotic hosts.

Nevertheless, archaea are a substantial constituent of plant-associated ecosystems in the aboveground and belowground phytobiome. Only a few studies have investigated the role of archaea in plant health and its potential symbiosis in ecosystems. This review discusses recent progress in identifying how archaea contribute to plant traits such as growth, adaptation to abiotic stresses, and immune activation. We synthesized the most recent functional and molecular data on archaea, including root colonization and the volatile emission to activate plant systemic immunity. These data represent a paradigm shift in our understanding of plant-microbiota interactions.

1. Introduction

Archaea were classified as the third domain of life along with prokaryotes and eukaryotes at the end of 1970 [1]. Archaea are subdivided into four superphyla: Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN); Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota (TACK); Euryarchaeota; and the newly discovered Asgardarchaeota [2]. Archaea were initially found in extreme environments with extreme conditions such as high salinity and high temperature, and environments in which they evolved to metabolize organics such as methane and nitrogen [3], [4]. In the tree of life based on metagenomes, archaea occur ubiquitously but are less prominent and less diverse in comparison with other microbes like bacteria, fungi, and viruses in several ecosystems, such as the terrestrial subsurface and human-associated microbiomes [5], [6].

Most metagenome-based microbiome studies focused on dominant bacteria and fungi rather than archaea. However, the accumulating evidence indicates that archaea are important constituents of plant microbiomes, sparking scientific interest in plant-associated archaea [7]. Previously, Archaea have been discovered in various land plant species, including rice, maize, and Scots pine, and in several aquatic plant species [8], [9], [10], [11] (Table 1). Archaea are primarily found in the plant rhizosphere, and have been identified at lower abundance in the endosphere and phyllosphere [12]. The abundance and taxonomy of archaea associated with plants differ depending on the plant species, environment, and developmental stage [13]. The combined results suggest that archaea might have developed specific plant-associated functions in plant ecosystems.

Table 1.

Potential functions of archaea in the plant phytobiome.

Archaea	Discovery location	Potential function	Reference
Crenarchaeota
	Mycorrhizospheres scots pine		[10]
	Rhizosphere of macrophyte Littorella uniflora	Ammonia oxidation	[24]
	Marine or wetland	Sulfur reduction (dissimilatory sulfite reductases)	[37]
Sulfolobus acidocaldarius		Indole acetic acid production	[41]
	Rhizosphere of Jatropha curcas	Nitrification	[48]
Thermoproteaceae, Sulfolobaceae Desulfurococcaceae		Bacteriosin or terpene in genome	[50]
Euryarchaeota
Methanogens, Rice cluster Ⅰ	Rice fields	Methane-oxidizing archaea	[3], [32], [59]
	Marine or wetland	Sulfur reduction (dissimilatory sulfite reductases)	[37]
	Forest and grassland soil	Phosphatase enzymes phoD and phoX	[26]
Halobacteria	Rhizophora mangle	Phosphorous solubilization	[27], [28]
Halobactierum Halococcus	Halonemum strobilaceum (Chenopodiaceae)	Phosphorous Solubilization	[27], [29]
Halolamina	Rhizosphere of grasses in hypersaline soil	Phosphorous solubilization	[27], [30]
Methanomicrobia, Halobacteriaceae	Rhizosphere of Bog vagetation	CO2 fixation, oxidative stress	[42]
Halococcus saccharolyticus, Halorubrum saccharovorum, Haloterrigena turkmenica, Halogeometricum sp., Natrialba sp	Marine salterns around the coast	Siderophores production	[9]
	Rhizosphere of Bog vegetation	Auxin biosynthesis	[42]
	Rhizosphere of Jatropha curcas		[48]
Methanosarcina	Rice paddy field	Hg-methylating	[8]
Pyrococcus furiousus	Cornus canadensis L. f. (ornamental dogwood)	ROS generation and detoxification	[16], [17], [60]
Halobacteriaceae		Terpene in genome	[50]
Thaumarchaeota
Nitrosocosmicus oleophilus MY3	Coal tar-contaminated sediment	Ammonia oxidation, growth promotion, disease resistance	[18], [61]
Non-classified
	Roots of Zea mays L.		[11]
	Rhizosphere of rice	Ammonia oxidation	[23]
	Soil from Bog vagetation	Oxidative stress	[42]
	Rhizosphere and phyllosphere of arugula	Oxidative stress	[7]

Two fundamental questions emerged about the interactions between archaea and plants. (1) What is the behavior of archaea during plant interactions? (2) What is the function of archaea within the plant health and growth? Some archaea have characteristics similar to bacteria, such as oxidizing ammonia and methane and environmental nutrient cycling [14]. The main characteristic of archaea that differentiates them from other domains is their viability in or adaptability to extreme environments [15]. This suggests that archaea might help plants adapt to abiotic stresses such as heavy metal contamination, high salinity, and high temperature [16], [17]. There is evidence that archaea are also involved in enhancing plant immune responses, such as triggering induced systemic resistance to pathogenic bacteria in Arabidopsis [18].

In this review, we discuss how archaea directly or indirectly affect plant health. We also consider how to maximize the potential of unique archaeal characteristics to optimize plant health.

1.1. How do archaea interact with plants?

Some archaeal species survive in both aerobic and anaerobic conditions. The plant-soil interface generally contains both aerobic and anaerobic zones. Anaerobic zones are generated when oxygen consumption by soil biota exceeds oxygen diffusion into the soil, or when air flow is restricted due to high moisture or high groundwater level [19]. Thus, the plant rhizosphere generates natural habitats for both aerobic and anaerobic archaea [20].

How do we know that archaea directly interact with plants and are not simply present in the rhizosphere? Previous study found archaeal cells exclusively colonizing and multiplying in plant roots without any soil components [18], [21]. In the absence of plants, no growth of these cells was detected. These results provide crucial evidence that archaea directly interact with plants in addition to colonizing the root surface. Subsequent sections of this letter will explore why archaea populate the rhizosphere and investigate their functional niche within plant ecosystems.

1.2. Archaea are involved in environmental nutrient cycling in plant ecosystems

Nutrient cycling within the soil environment is mediated by microbes and their interactions. Plant roots absorb nitrogen (N) from the soil in the form of ammonium (NH⁴⁺) and nitrate (NO^3–). However, the predominant form of N absorbed by plant roots is NO^3–, which indicates NH⁴⁺ and atmospheric dinitrogen (N₂) should be reduced [3] (Fig. 1a). These N-cycling processes are mediated by ammonia-oxidizing bacteria and ammonia-oxidizing archaea (AOA) [22]. In rice soils AOA were more abundant in the rhizosphere than in bulk soil, indicating that AOA-mediated N-cycling is primarily associated with the plant root [23] (Table 1). The ammonia monooxygenase (amo1) genes of Crenarchaeota were strongly enriched in the rhizosphere of the submersed macrophyte Littorella uniflora compared to the levels in surrounding sediments [24] (Table 1). These observations suggest that AOA are enriched in the plant rhizosphere and are involved in N-cycling to support plant growth and health.

Fig. 1.

Archaea are involved in environmental nutrient cycling in plant ecosystems. (a) Archaeal ammonia monooxygenase (amo1) gene catalyzes the oxidation of ammonium (NH⁴⁺) to nitrite (NO^2–), which is subsequently oxidized to NO^3–, the bioavailable form of N that plants utilize. (b) The alkaline phosphatase (Pho) genes of archaea hydrolyze soil organic-P to HPO₄^-2 and H₂PO₄^-1, which can be absorbed by plant roots. (c) Methyl-coenzyme M reductase (Mcr) catalyzes the last step in methanogenesis (CH₄ synthesis) and the first step in methanotrophy (CH₄ oxidation). Methanogenic archaea with high abundance of mcr are involved in C cycling. (d) S in the soil primarily exists in the form of sulfate-esters (-O-SO₃H) and sulfonates (C-SO₃H), which are reduced to bioavailable sulfides (SO^4-) for plant utilization by archaeal dissimilatory sulfite reductases (dsr).

Phosphorous (P) is another important element in plants. Plants and microbes obtain soluble organic-P from soil by hydrolyzing inorganic-P to orthophosphate [25]. Although both plant and microbial phosphatases effectively solubilize orthophosphate from soil organic-P, microbial phosphatases display higher efficiencies than those of plants [25]. Bacteria and archaea contain alkaline phosphatases PhoD and PhoX, which hydrolyze soil organic-P [26] (Fig. 1b). Previous studies showed that Euryarchaeota isolated from arable, forest, and grassland soil expressed phoD and phoX genes implying P hydrolyzing around plants [26] (Table 1). Indeed, some of Euryarchaeota isolated from plant rhizosphere had measureable P solubilization activity [27], [28], [29], [30] (Table 1). Further studies are needed to determine whether archaeal P solubilization contributes to and supports plant growth.

Carbon (C) cycling is crucial for plant ecosystems. Archaea are involved in C cycling by generating methane (CH₄) using H₂, CO₂, or methylated compounds (Fig. 1c) [31]. Previous studies showed that archaea were highly abundant in rice fields, which contribute 10–25% of global methane emissions [32] (Table 1). Methanogenic archaea of the Euryarchaeota phylum produce up to 60% of this methane emission [33]. Methyl-coenzyme M reductase (Mcr) is commonly expressed in methanogenic archaea; this enzyme catalyzes the last step in methanogenesis (CH₄ synthesis) and the first step in methanotrophy (CH₄ oxidation) [31]. Methanogenesis and methane oxidation are important steps in the C cycle, and both are performed exclusively by anaerobic methanogens [34].

Some bacteria and archaea are involved in sulfur (S) cycling, which is an important element in organisms [35]. Sulfur in the soil exists primarily in the form of sulfate-esters (-O-SO₃H) and sulfonates (C-SO₃H), which need to be metabolized by soil microbes before the S becomes bioavailable for plants [36]. Archaea reduce these sulfates and sulfites to sulfides via enzymes encoded by the dissimilatory sulfite reductases (dsr) gene cluster [37] (Fig. 1d). Euryarchaeota, Crenarchaeota, and Aigarchaeota isolated from marine habitats or wetlands express the genetic capacity to reduce sulfite to sulfide via dsr [37] (Table 1). The combined studies suggest a potential role for archaea in rhizospheric S cycling, although further work is needed to verify direct archaeal involvement in S cycles.

The emerging evidence makes us expect that archaea interact with the land plant through soil nutrient cycling. However, even if archaea have the ability to circulate nutrient, it cannot be concluded that it makes plants healthy. For example, it has been suggested that AOA can result in inorganic N leaching from the soil, becoming less available to plants [38]. In addition, there is a report that ammonia-oxidizing bacteria present on the surface is primarily involved in regulating soil nitrification, but not AOA [39]. We further discuss in the following paragraphs how archaea positively affect plant health by nutrient cycling or others.

1.3. Plant growth-promoting archaea

Plant growth-promoting rhizobacteria (PGPR) promote plant growth by directly or indirectly interacting with plant roots [40]. There are some studies that archaea are also considered as plant growth-promoting archaea (PGPA). For example, Nitrosocosmicus oleophilus MY3 cells promote Arabidopsis growth by oxidizing N into plant-bioavailable forms [18] (Table 1). Some halophilic archaea isolated from marine salterns around the Bhavnagar coast showed functional signatures of P siderophore production [9] (Table 1). Some of these archaeal species were found in terrestrial plants, and it is likely that they might support plant growth by facilitating plant iron uptake [29] (Fig. 2 and Table 1).

Fig. 2.

Beneficial effects of archaea around plants. Archaea enhance plant health by promoting growth, inducing resistance, and elevating abiotic stress tolerance. Nutrient (N, C, P, and S) cycling and siderophore production by archaea could provide nutrients that support and promote plant growth. Indole acetic acid (IAA) produced by archaea and the genetic capacity for auxin biosynthesis in archaea also function to promote plant growth. N-acyl-L-homoserine lactones (AHLs) produced during Archaea’s cell-to-cell communication may also affect plant growth and defense mechanisms. The as-yet unidentified volatile organic compounds (VOC) of archaea trigger plant growth and induced systemic resistance. Archaea can stabilize toxic metal via the dissimilatory sulfate reduction process, thereby supporting plant growth under environmental conditions with high metal levels. Functional signatures for resistance to oxidative stress and production of reactive oxygen species (ROS) suggest that archaea could protect plants under abiotic stress conditions.

PGPR also regulate plant growth by modulating hormone production, and archaea have a similar potential. Early studies reported that archaea promote the secretion of plant hormones. Thermophilic Sulfolobus acidocaldarius produces the plant growth-promoting hormone indole acetic acid (IAA) at levels a thousand times higher than that observed in typical plant extracts [41] (Fig. 2 and Table 1). This was one of the first reports linking archaea to plant growth promotion [41]. A recent metagenomic analysis of archaea associated with bog vegetation detected genetic evidence for auxin biosynthesis, which further supports the plant growth-promoting activity of archaea [42] (Fig. 2 and Table 1).

N-acyl-L-homoserine lactones (AHLs) are used by cell-to-cell communication of Gram negative bacteria such as Pseudomonas [43]. AHLs can be recognized by plants, It modulate plant defense and plant growth responses [44]. Recently, there are also increasing reports of the potential for archaea to be involved in cell-signalling [45]. The evidence that archaea join the conversation was found by detecting of AHL-like activity across a range of archaeal isolates [45]. Perhaps some form of archaeal signalling may help modulate plant-archaea interactions and plant growth promotion like gram negative bacteria did (Fig. 2).

A recent study showed that N. oleophilus MY3 cells promote the growth of Arabidopsis plants grown on soil and in hypotonic medium [18]. Treatment of plants with volatile organic compounds (VOC) derived from N. oleophilus MY3 cells could also promote growth in the absence of any direct physical contact between archaea and plants [18]. These results indicate that archaeal VOC have a key role in plant growth promotion similar to that of PGPR. Archaeal VOC did not contain 2,3-butanediol, which is a well-known bacterial VOC that promotes plant growth [18], [46]. These observations lead to another emerging area of research, which investigates the effects of archaea or archaeal VOC in plant growth promotion and host-microbe interactions.

1.4. Archaea are involved in enhancing abiotic and biotic stress resistance

Archaea can live in environments with extreme conditions, such as extremes of temperatures, salinity or pH [47]. The hyperthermophilic archaea Methanopyrus kandleri live at 121℃, whereas the acidophilic archaea Picrophilus survive at pH 0.06 [47]. Plants can also grow in environments with high levels of abiotic stress. Metagenomic analysis of the rhizosphere of Jatropha curcas, which adapted to grow under salt stress and high temperature conditions, showed high abundances of Crenarchaeota and Euryarchaeota [48] (Table 1). Although the detailed reason is not known, Crenarchaeota and Euryarchaeota may help the Jatropha curcas adapt to salt stress and high temperature condition.

Euryarchaeota and Methanosarcina species can methylate mercury (Hg) in rice fields, suggesting that these plant-associated archaea might have important roles in supporting plant growth under high Hg conditions [8] (Table 1). Sulfate-reducing organisms stabilize metals such as Pb, Zn, and Cd in soils [49]. Bacterial and archaeal dsrA/B genes are key factors in metal sulfide formation via the dissimilatory sulfate reduction process [37]. Therefore, archaea could support plant growth under adverse environmental conditions with high metal levels (Fig. 2). Further, the metagenome analysis of archaea from alpine bogs suggest functional potential in protecting plants from oxidative and osmotic stresses [42] (Table 1). Archaea found in the rhizosphere and phyllosphere of arugula also displayed functional signatures for resistance to oxidative stress (Table 1) [7]. These combined results suggest that archaea could help plants survive and adapt to abiotic stress conditions (Fig. 2).

Archaea display functional traits that might enhance plant responses to biotic stresses. Genome analyses of 203 archaea species including Crenarchaeota and Euryarchaota showed that genes involved in terpene and bacteriocin production were widely distributed in Crenarchaota genomes [50]. Terpene and bacteriocin deter herbivore feeding and microbial colonization, respectively; therefore, these archaea have potential functions for plant defense responses against herbivores and pathogenic bacteria [51], [52].

Arabidopsis plants exposed to N. oleophilus MY3 cells displayed enhanced disease resistance when subsequently challenged with Pectobacterium carotovorum and Pseudomonas syringae [18]. This induced resistance response depends on jasmonic acid rather than salicylic acid, indicating that archaea triggers induced systemic resistance (ISR) in Arabidopsis. NO₂⁻ promotes ISR in plants. However, the ISR response still occurs when archaea are completely sequestered from the plants, suggesting that archaeal volatile compounds elicit ISR responses against pathogens [18]. These combined results suggest that archaea could produce novel plant protection compounds and could be used in innovative biotechnological applications.

1.5. Colonization and role of plant-associated archaea in the seeds

Archaea have a variety of properties that benefit the host plant and may support the plant progeny. In tomato (Solanum lycopersicum L.), beneficial bacteria are actively transmitted by the plant to the next generation via the seeds [53]. Although plants do not actively select and transmit archaea to the offspring, recent work detected archaeal abundances of up to 3.09 X 10⁹ copies g⁻¹ in seeds of native alpine plants [54]). Interestingly, in alpine seeds the composition of Archaea was highly specific for each plant species, which may suggest a co-evolution in native environments [54]. Studies on transmission via clonal colonies in Glechoma hederacea also did not detect archaeal transmission from the mother to the daughter plant [55]. In seeds, archaea appear to have evolved into bystander organisms based on synthrophic interactions with bacteria [56]. Instead, root exudates serve to attract and enrich archaea from the surrounding soil to the plant rhizosphere [57]. This archaeal colonization occurs during the latter phase of plant development [58]. However, more studies are necessary to understand the co-evolution between plants and Archaea and their transmission routes.

2. Conclusions and perspectives

This study discussed the beneficial functions of archaea for plant health. Archaea have been detected in plant tissues and on plant surfaces. However, most of the studies on plant-archaea interactions are limited to metagenome analysis and only suggest the possibility that archaea have on plants, but do not suggest how archaea directly affect plants. Recently, there is one study about nitrogen-oxidizing archaea function to plants, they reported that archaea promote plant growth and enhance resistance to biotic stresses [18].

Although many studies have yet to be conducted, we believe that these findings show the potential of archaea as a biostimulant and bioprotectant. Archaea have very slow growth rates, which makes archaeal genetic engineering a more suitable biotechnological strategy than direct field applications of archaea as biocontrol agents. The plant’s usefulness of archaea can also be inferred through genetic studies of archaea. There is some research on the application of archaeal genetic engineering to plant cells. Superoxide reductase (SOR) gene isolated from the thermophilic archaea Pyrococcus furiousus has been successfully expressed in Arabidopsis and tobacco cells; these transgenic plants displayed higher tolerance to heat, light, and methyl viologen than non-expressing plants [16], [17]. SOR expression in the chloroplast could further enhance plant stress tolerance, as a significant proportion of reactive oxygen species are generated in the chloroplast [16]. Archaea themselves are expected to have many beneficial properties for plants that have not yet been identified due to experimental and technical challenges. Further work is needed to cultivate and analyze plant-associated archaea and to determine their full potential in supporting plant health and growth. Today we have no single isolate of a plant-originated Archaeon, therefore, cultivation of an archaea as a plant endophytes is important for further plant-archaea interaction studies [57]. We predict that this work will greatly expand their beneficial applications for agriculture.

3. Summary statement

Archaea is an important division of life forms on earth. While archaea are highly abundant in extreme and normal environments, scientists have not been much attention, especially in association with eukaryotic hosts. Here we give recent evidence that archaea are members of plant microbiome. Archaea’s beneficial effect was focused on plant growth promotion, elicitation of abiotic tolerance, and induced plant immunity. Our review paves a new way to increase crop productivity with Archaea.

4. Availability of data and materials

All figures and tables of this letter are available in manuscripts.

5. Ethics approval and consent to participate

Not applicable.

6. Consent for publication

Not applicable.

Author contributions

J.J., J.-S. K., J.T., G. B., and C-M.R. wrote the manuscript.

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.